How They Discovered the Truth
by Baileys
Summary: Continuing my S9 Nature of the Beast Obsession. This intersects right between my prequel 'How they all found out' and my epilogue 'How they got Lucky'. This is the CASE bit of the episode that was missing. Featuring the team!
1. Chapter 1

Dis: Not mine. Sooo wish etc…

Summary: Continuing my S9 Nature of the Beast Obsession. This intersects right between my prequel 'How they all found out' and my epilogue 'Lucky'. This is the CASE bit of the episode that was missing. Featuring the team! (SPOLIERS for season 9)

"Boss, thought you were at the hospital?" McGee spoke before he could think better of it.

He left the witness he'd been interviewing and fell into step with his boss when Gibbs ducked under the crime scene tape.

"I was."

McGee caught the evidence bag Gibbs thrust at him, clasping it in both hands against his chest.

"Bullet from Tony's vest?"

"How's Tony?" Ziva pounced the minute she saw Gibbs.

McGee listened in as he wrote chain of evidence on the baggy and slipped it into his pocket.

"Unconscious." He heard Gibbs reply. "Ducky's with him."

McGee looked up sharply at the weary tone. It didn't take a very special agent to hear what wasn't being said. Gibbs was worried. If Gibbs was worried things were far worse with Tony than any of them could imagine.

"Anything we can do boss?" McGee wanted to fill the cold stony silence that lasted far longer than was comfortable.

For his trouble McGee got a glare in return and gave himself a mental head slap. His job was the best thing he could do right now. Find out the answers to the many questions that had been unanswered over the last couple of months. Tony's assignment. That was what had led them here, to investigate the shooting of one of their own.

Gibbs turned away from him and stared at the spot, outlined in chalk by the LEO's of the position Tony had been found. McGee was just glad they weren't looking at his body, but somehow he thought Gibbs was imagining just that.

"Tony was found lying face down. Gun drawn. One bullet to the chest. We've recovered the shell casing." McGee recited the information as calmly as he could.

Gibbs said nothing and moved on to the look at the rest of the scene. McGee shared a concerned look with Ziva before following. McGee saw Gibbs' gaze settle on a patch of blood on the ground that had already been marked.

"There a body?"

"Not yet." McGee swallowed. "But by the amount…" He fell silent.

It made very little sense. If Tony had got a shot in before he was hit then the body should still be here.

"We found two more shell casings." Ziva broke into his thinking, pointing at the other two marks in the alleyway.

McGee studied Gibbs as he stood and looked around at the dark, secluded alley. Fear, loss, concern. He saw all these emotions cross his bosses face and in that instance felt an irrational annoyance build up within him. McGee didn't often get angry, not in the 'I want to punch someone' sense, but it seemed this was a special occasion. Only the one he wanted to punch was Tony. Gibbs looked broken and it was all Tony's fault.

"He was following orders Tim." Gibbs spoke the words without breaking from his contemplation of the scene. "I'm heading back to the hospital." He walked away before McGee could ask how in hell he'd known what he was thinking.

"I'll call as soon as we have anything boss." McGee threw out to his retreating back.

When he turned around, anger at Tony forgotten and shocked expression still in place Ziva was smiling at him.

"As Tony would say" she shrugged, "he's Gibbs."


	2. Chapter 2

"He awake yet, Duck?"

Gibbs stormed up the corridor towards Ducky who was just shutting the door to Tony's room.

"Regained consciousness a few minutes ago. Past the standard tests." Ducky replied stoically.

The tone alone was enough to set Gibbs' gut on high alert. "What?"

Ducky seemed to take a breath before he answered. "McGee has called. They found a body."

Gibbs pulled out his cell and growled at the number of missed calls.

"Go." He said resisting the urge to make a cell phone sized dent in the hospital's wall. "I'm staying here."

Ducky nodded, patting his arm in acknowledgment of the upset Gibbs knew he was failing not to show. Once Ducky was on his way Gibbs focused on the door to DiNozzo's room. He couldn't walk in like this. First McGee was reading him like a book then Ducky was being succinct! Everything was upside down and sideways. They couldn't continue this way. DiNozzo had had the whole team acting out of sorts through worry and now he goes and lands himself in hospital! Gibbs felt the rage build within him and sort to hold onto to it. It had chased away the fear that had been holding residence within him since he'd first suspected anything about Tony's secret assignment. Gibbs swung open the door.

"Hey boss."

His anger fled like a scared animal at Tony's soft call . Gibbs deftly tried to maintain a neutral face, but the relief at hearing that voice brought back the fear that he'd come close to losing something special tonight.

"Good to hear your voice DiNozzo." Gibbs managed eventually.

Tony, eyes closed again, chuckled briefly. "Never thought I'd hear you say that."

The voice was weak and lacked it's usual energy. Gibbs moved quickly over to the bed and looked down at his agent, examining the bruise on Tony's forehead. Tony didn't flinch when Gibbs grasped his chin and moved his head into the dull light of the lamp, but he did open his eyes.

"I'm all good boss."

Gibbs gave him an 'are you kidding me?' glare that would normally slide right off him, but this time Gibbs saw wide eyed fear. Immediately sitting down on the edge of the bed and closing the distance between them Gibbs placed one warm palm on the side of Tony's face, forcing him to look at him.

"What's wrong?" Besides the obvious of course, but Gibbs knew Tony understood him.

"What happened?" Tony said, his voice breaking.

"Was hoping you could tell us." Gibbs said warily.

"I don't remember anything."


	3. Chapter 3

Tony had panicked after admitting to not remembering much from the last few months. Gibbs tried to calm him down by dishing out as many meaningless platitudes as he could remember before the tears forming in overly bright green eyes had a chance to fall. The more upset DiNozzo got the more he could feel himself about to lose it. Nothing it seemed was normal today and in a strange way that made Gibbs feel better for being so far off his game. Tony eventually got control and slipped into silence, Gibbs took the opportunity to step out and make a phone call. Door closed Gibbs removed the cell from his pocket and ignored a nurses glare as he proceeded to punch in the right number.

"McGee tell me you have something." He barked into the receiver as soon as he heard the click of connection.

To his credit McGee didn't miss a beat. "Ducky's taken the body back to autopsy. Ziva has already returned to the Navy Yard and taken evidence to Abby. I'm on my way back now with casings from where the body was dumped." McGee paused. Scared to say the next thing. "Boss, the body. It's Cade."

Gibbs closed his eyes slowly. He was afraid of that. The anger was back, a fire ball burning within him, drawing energy from his need to hold accountable those who had hurt HIS agent.

Tony had come to him a few weeks ago, with Barratt in tow, they had been targeted and needed his help. He'd been his usual controlled self back and hidden his worry and anxiety at hearing how someone had tried to take them out so well that even Tony managed to relax that night and let his guard down. Barratt had stayed in the guest room, which had left him and DiNozzo downstairs. With no boat or other pursuits to concentrate on Gibbs had found himself awake most of that night, sitting in the chair watching DiNozzo snore on his sofa. It was stupid, but after months without contact Gibbs was reluctant to sleep. It was the beginning of the end of Tony's assignment and he had no control over any of it. That had pissed him off the most.

"I need to know everything McGee." He didn't need to tell McGee that this was to be kept as low key as possible, that the evidence needed to be processed within record time.

"Boss what has Tony said?"

"He's said nothing McGee. He doesn't remember." With that Gibbs flipped his phone shut and dialled another number, a person who he trusted, someone who he hoped could help save his agent.


	4. Chapter 4

McGee entered Abby's lab carrying the bullets Ducky had taken out of Cade and the first thing he noticed was the silence.

"You heard?" He asked as soon as he stepped through her door.

Abby looked solemn. He had not been a fan of Cade, for obvious reasons, but McGee wasn't petty, he knew Abby had really liked him.

"You remember when you said you hoped it was no one we knew?"

McGee could see where she was going with this and instead of an answer he gave her a hug.

"I mean I know we don't know anything, but why else would Tony and Cade be together in that alley? Cade sent me that message and-"

McGee pulled away and shoved the bullets into her hand. "Abby we don't have time. I'm sorry. But you want answers. Gibbs wants answers. You process this and we will get answers."

It was clearly not what Abby wanted to hear.

"One of my bestest friends has possibly killed another friend." Abby inhaled sharply, as if realising what she had just said. "But why would Cade shoot at Tony? It doesn't make sense."

No, it didn't make sense. Right now they had no idea who shot at who. One agent in the hospital and one agent dead, a tampered with crime scene and a seriously distracted Gibbs made a sure recipe for disaster. And lucky him, he was in charge of fixing it. What he wouldn't give to be Probie again for real.

"I know." He answered succinctly instead. "But until we get the answers to what happened Gibbs is going to be going crazy. Tony's lost his memory-"

"What?" Ziva interrupted walking into the lab, Ducky and Palmer following soon after. "Tony can't remember what happened?"

"Gibbs didn't say much. Just that Tony doesn't remember anything."

"Anything as in doesn't know who he is or doesn't remember anything like Gibbs didn't before he left for Mexico?" Abby asked him, clearly getting worked up.

A worked up Abby was probably better than a solemn Abby in any case.

"Gibbs didn't say." He sighed.

"McGee you should have asked!" Abby punched him. Hard. "I'm calling him." She took out her cell and pressed her speed dial.

"Abigail." Ducky chastised, removing the phone from her palm. "Jethro is at the hospital. He has enough to deal with right now. And we have our jobs to do if we are to help young Anthony out of this mess he's found himself in."

"Ducky's right." Ziva piped up. "Tony is safe for now, but we need to prove what happened in that alley, somebody shot at Tony and killed Cade."

"What if Tony killed Cade." McGee spoke thoughtlessly.

Abby punched him again. "I will not believe that."

"I recovered three bullets of different types from Agent Cade's body. Only one bullet delivered the kill shot, the other two were post mortem." Ducky pointed at the evidence bag Abby held.

"If I can match the kill shot to the bullet from Tony's vest-"

Abby was interrupted by one her machines beeping. McGee and the rest watched as she typed away on her keyboard.

"There were three different blood types at the scene." Abby smiled. "I'm running the DNA through AFIS."

"Three?" Ziva queried.

"Well assuming Cade was one, and Tony's another-"

"The third could be our killers." Ducky finished.

"Tony's weapon discharged twice." Abby confirmed.

McGee was aware they weren't exactly being objective and was sure, had this been anyone else, Gibbs would have slapped him silly by now, but it was the middle of the night, they were all exhausted and Tony wasn't just anyone.

"Let's hope-"

The computer pinged three times and the three matches appeared on the plasma screen. McGee froze along with everyone else in the room as they looked at the three very familiar faces of Cade, Tony and EJ Barrett.

"This isn't good is it?" Palmer spoke for the first time .

"No, Mr Palmer. It is not."


	5. Chapter 5

Gibbs paced the hall for the umpteenth time that hour. Hospital staff were really starting to hate him he noted, but he genuinely didn't give a damn. Dr Cranston had basically kicked him out and he had no where else to be.

Gibbs glared at the closed door and hoped to God she was making some progress. A response to trauma. The words echoed in his head. Gibbs had seen Tony vulnerable plenty of times, but never quite as lost as this. The plague, killing Jeffery White, even in the jail cell Tony had kept the 'DiNozzo' about him, he never hid from Gibbs and wasn't afraid to ask for affection or attention when he needed it. It was a trait Gibbs actually admired and respected despite never telling him. Being able to trust someone enough to show them your insecurities was a monumental thing. Being the one trusted was one of the greatest gifts Gibbs felt he could ever be given.

This time though, something was different. DiNozzo was closed. He was hiding. Afraid. Never a word Gibbs would associate with him. If DiNozzo wasn't going to willing show him what was wrong then Gibbs had very little hope in helping him. Which he why he'd made the call to Cranston.

His phoned buzzed, reading the ID he answered immediately. "What you got McGee?"

Gibbs listened as McGee reeled off the evidence collected and analysed. The information on Barrett didn't surprise him like it had the rest. He had tried contacting her on his way to the hospital to no avail and was honestly now fearing the worst. Rule 12. He should have been harder on Tony, made him see that he wasn't trying to be a hardass. He was trying to be a dad. Although even he couldn't have known this would be how it would turn out.

Gibbs ended the call in his usual manner, ordering McGee to get the answers and get them fast, hanging up before hearing the patented 'on it boss'. Processing what he'd just heard. Putting it together with the preliminary autopsy results Ducky had reported to him earlier. He wanted to go back in and question DiNozzo, but knew an interrogation was not going to help and he would only get his ass thrown out by the doctor again.

They had more questions than answers, and nothing was adding up. Why was the body moved? Why the two shots post mortem? Why a different gun? Gibbs could hazard a guess at at least two of those, but Gibbs wasn't one for guessing. His gut was churning as it did when something wasn't sitting right, however it wasn't helping him find the right direction to pursue. Gibbs admitted, to himself at least, that maybe he was just too close to this. There was a reason victims families were kept on the other side of the crime tape. Talking about breaking rules, he'd gone and broken another for DiNozzo. It brought into question his judgement on whether they should even be the team investigating this case. When DiNozzo had been accused of murder, the first time, he'd agreed to Fornell running it, but back then DiNozzo had had all his faculties and no secrets to hide. Currently DiNozzo had been missing for months, working in secret and now no memory to explain himself.

Which brought him back to glare at the closed door and hope like hell Dr Cranston would succeed where he had so far failed.

"Agent Gibbs?" Gibbs turned to see a nurse holding out a pen and sheet of paper. "We need you to fill in Agent DiNozzo's admittance and conditional release forms."

Gibbs nodded mutely and took the forms and the pen over to the nurses desk to fill out.


	6. Chapter 6

It was still dark outside when McGee returned to the Bullpen, only to find Ducky sitting at Tony's Desk.

"Ducky, you ok?"

Ducky looked over at him, pausing before he spoke. "I don't believe so my dear boy."

McGee swallowed. "Tony?"

When Ducky looked immediately guilty McGee actually felt like throwing up, but the urge was quickly quash by Ducky hastily reassuring him that last he heard Tony was doing just fine.

"I'm very sorry, I didn't mean to cause upset." Ducky finished, leaning back in Tony's chair in a very 'DiNozzo' way. "I've just got no where else to be. Autopsy can be a very lonely place and that isn't ideal in times of family crisis."

"I no what you mean." McGee replied, voice distant.

He'd been looking at Tony's empty desk a lot over the last few months. The fact that they didn't know from one day to the next if Tony would be joining them or not had been disconcerting. But when he'd not been seen for the fifth day on the run, well that's when McGee, along with Ziva and Abby had decided to do some secret snooping of their own. They'd turned up nothing, the bullpen camera footage had left little to be desired. He remembered almost hoping Tony would catch them spying on him. Call him a McName and return the normalcy.

"Anthony is very resilient Timothy. Gibbs will make sure he returns to us safe and sound." Ducky's soft voice resounded across the quietness the office.

With the lights dimmed, the sounds of humming computers and Ducky's softy spoken words nearly had him drifting off to sleep. Safe and sound. It made Tony sound like something delicate and DiNozzo certainly couldn't be described as delicate. Unstable? Sure. Tony was insane, that had been confirmed many times, most notably when he actually declared his thoughts to Gibbs after speaking with Tony in MTAC when he was agent afloat. Gibbs had responded with an emphatic 'Oh yeah!' As if Tony's insanity was never in question.

"I hope so Ducky." McGee responded just as softly. "I've actual missed him."

He heard Ducky chuckle. "Haven't we all."


	7. Chapter 7

Gibbs had immediately called Fornell after his encounter with Agent Stratton. He wasn't exactly receptive to being awoken in the middle of the night, but as soon as he mentioned DiNozzo Fornell had given up any hope of convincing him to wait until morning. Fornell said he'd make some calls and get back to him. Gibbs cell rang immediately after hanging up.

"Gibbs Gibbs Gibbs!" Abby shouted down the line, pulling Gibbs' usual trick.

"What ya got Abs?"

Abby had matched the bullets. DiNozzo's gun didn't deliver the kill shot. But someone was trying to make it look like he had. The badge in DiNozzo coat, the use of his gun on Cade's body post mortem. Wasn't this the forth time Tony had been framed for murder? It wasn't a very good attempt, more like a temporary distraction to throw them off so the real killer had time to cover his tracks. Gibbs' gut was churning, afraid it may well have worked too. Tony was definitely wrapped up in something big, had no memory and it wasn't over yet.

His phone buzzed again, a hang up from Dr Cranston. Gibbs ran full pelt back to the room only to meet the doctor in the hallway.

"He's in the bathroom." She announced on his approach.

"Called to say he'd gone to the head?" Gibbs snapped, in full protective mode.

"You know an Agent Stratton?" She asked completely ignoring his tone.

"What?" The hairs on the back of his neck stood instantly on end. "He was here?"

"Came into the room. Tony's reaction was… troubling."

Gibbs rubbed a hand through his hair, looking around the corridor door for any sign of Stratton. "What happened?"

"Well I think he was surprised to see somebody with him, made an excuse and left."

"Stay with DiNozzo." Gibbs ordered.

Dr Cranston narrowed her eyes. "You know him?"

"I have to call Fornell ." Gibbs stormed off back down the corridor.


	8. Chapter 8

McGee picked up his phone on the first ring.

"McGee I want agents outside DiNozzo's room NOW!"

"Boss what's wrong?"

"Do it McGee!"

Gibbs hung up, leaving McGee staring at his cell.

"What was that about?" Ziva asked him from across the bullpen.

"Gibbs wants protection outside Tony's hospital room."

"Tony is in danger?"

"Gibbs must think so." McGee said blankly.

"Well what are you waiting for?" Ziva shouted, drawing the attention of the few agents unlucky enough to still be around at this hour.

"Right, of course." McGee stopped staring at Tony's empty desk and put the request through.

McGee called Gibbs back to tell him which agents were on route. He tried asking for more details, but Gibbs clearly wasn't in a talking mood because he hung up before McGee could get to the end of the question.

"We should go down there." Ziva said, standing and grabbing her coat.

"No." McGee forced out. "We stay and finish up. We still don't know where Barrett is and we don't know who shot Tony or Cade."

"We know nothing McGee." Ziva emphasised, throwing her coat back down. "We've processed all the evidence and have no other leads. If there was another shooter then they have left no face."

"Trace."

"That too."

McGee thought over her argument. "You think EJ shot Tony?"

Ziva tried to look a little guilty. "It is a possibility is it not? She was Tony's target-"

"We don't know that."

"What about the autopsy tape. Removing a microchip from Levin's arm? Then immediately after Tony is sent on a secret mission that we are to know nothing about. I can only think of one reason for that."

"Coincidence."

"If Gibbs could hear you-"

"I know!" McGee threw his hands over his head.

"Okay, we finish here, get Abby then we'll go to the hospital. But I'm not facing Gibbs until we have the answers."

Ziva smiled. "Ok, McGee."


	9. Chapter 9

Gibbs stormed the corridors looking for any sign of Stratton. He checked cupboards, elevators and stairwells, but came up empty. He should have told McGee to get a hold of the hospital camera footage. He wanted on I.D on Stratton. After placing his second call to Fornell, only to discover that nobody knew of an agent Stratton, Gibbs didn't need to put two and two together. He already knew in his gut whoever Stratton was he was a threat to his agent.

Mind wandering back to his previous conversation with his team he knew they were running out of time. They needed an I.D on the killer. This case needed to be closed, or as close to it, by daylight, otherwise Vance would have it taken out of their hands and DiNozzo could find himself exiled from the team once again, pending a psych review. SecNav had a hell of a lot to answer for.

He was going to get in trouble for not reporting the shootings to the Director straight away, but it was a risk he was more than willing to take. Tony had been taken away from them too many times. Secret undercover ops and reassignments. Gibbs was getting him back and this time he would be keeping him.

The agents McGee had sent were arriving, Gibbs briefed them and took that as his cue to push things along. They needed answers and there was now only one person that he believed was able to give them. Gibbs approached the door he'd been glaring at most of the night, pushed down on the handle and walked on in.

End of pt2.

The story continues in the already posted and recently added to tag 'How they all got Lucky'.

Thanks for reading until the end! ;)


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